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Vol. 12, Issue 2, 323-337, February 2001
and#
*Whitehead Institute for Biomedical Research, Nine Cambridge
Center, Cambridge, Massachusetts 02142; We used genome-wide expression analysis to explore how gene
expression in Saccharomyces cerevisiae is remodeled in
response to various changes in extracellular environment, including
changes in temperature, oxidation, nutrients, pH, and osmolarity. The results demonstrate that more than half of the genome is involved in
various responses to environmental change and identify the global set
of genes induced and repressed by each condition. These data implicate
a substantial number of previously uncharacterized genes in these
responses and reveal a signature common to environmental responses that
involves ~10% of yeast genes. The results of expression analysis
with MSN2/MSN4 mutants support the model
that the Msn2/Msn4 activators induce the common response to
environmental change. These results provide a global description of the
transcriptional response to environmental change and extend our
understanding of the role of activators in effecting this response.
Department of
Biology, Massachusetts Institute of Technology, Cambridge,
Massachusetts 02139; and ¶Howard Hughes Medical Institute,
Department of Molecular Genetics and Cell Biology, University of
Chicago, Chicago, Illinois 60637
These authors made equal contributions.
Present addresses:
MRC Clinical Sciences Centre,
Imperial College School of Medicine, Hammersmith Campus, Du Cane Road,
London W12 ONN, UK;
§LG Chemical Ltd., Research Park,
104-1, Moon Ji-Dong, Song-Gu, Taejon, Korea.
#
Corresponding author. E-mail address:
young{at}WI.MIT.EDU.
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A. A. Petti and G. M. Church A network of transcriptionally coordinated functional modules in Saccharomyces cerevisiae Genome Res., September 1, 2005; 15(9): 1298 - 1306. [Abstract] [Full Text] [PDF]
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I. Bourges, S. Horan, and B. Meunier Effect of Inhibition of the bc1 Complex on Gene Expression Profile in Yeast J. Biol. Chem., August 19, 2005; 280(33): 29743 - 29749. [Abstract] [Full Text] [PDF]
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K. Rothfels, J. C. Tanny, E. Molnar, H. Friesen, C. Commisso, and J. Segall Components of the ESCRT Pathway, DFG16, and YGR122w Are Required for Rim101 To Act as a Corepressor with Nrg1 at the Negative Regulatory Element of the DIT1 Gene of Saccharomyces cerevisiae Mol. Cell. Biol., August 1, 2005; 25(15): 6772 - 6788. [Abstract] [Full Text] [PDF]
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D. J. Krysan, E. L. Ting, C. Abeijon, L. Kroos, and R. S. Fuller Yapsins Are a Family of Aspartyl Proteases Required for Cell Wall Integrity in Saccharomyces cerevisiae Eukaryot. Cell, August 1, 2005; 4(8): 1364 - 1374. [Abstract] [Full Text] [PDF]
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S. Claret, X. Gatti, F. Doignon, D. Thoraval, and M. Crouzet The Rgd1p Rho GTPase-Activating Protein and the Mid2p Cell Wall Sensor Are Required at Low pH for Protein Kinase C Pathway Activation and Cell Survival in Saccharomyces cerevisiae Eukaryot. Cell, August 1, 2005; 4(8): 1375 - 1386. [Abstract] [Full Text] [PDF]
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N. Bing and I. Hoeschele Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference Genetics, June 1, 2005; 170(2): 533 - 542. [Abstract] [Full Text] [PDF]
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L.-C. Lai, A. L. Kosorukoff, P. V. Burke, and K. E. Kwast Dynamical Remodeling of the Transcriptome during Short-Term Anaerobiosis in Saccharomyces cerevisiae: Differential Response and Role of Msn2 and/or Msn4 and Other Factors in Galactose and Glucose Media Mol. Cell. Biol., May 15, 2005; 25(10): 4075 - 4091. [Abstract] [Full Text] [PDF]
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C. Tachibana, J. Y. Yoo, J.-B. Tagne, N. Kacherovsky, T. I. Lee, and E. T. Young Combined Global Localization Analysis and Transcriptome Data Identify Genes That Are Directly Coregulated by Adr1 and Cat8 Mol. Cell. Biol., March 15, 2005; 25(6): 2138 - 2146. [Abstract] [Full Text] [PDF]
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J. Panadero, F. Randez-Gil, and J. A. Prieto Validation of a Flour-Free Model Dough System for Throughput Studies of Baker's Yeast Appl. Envir. Microbiol., March 1, 2005; 71(3): 1142 - 1147. [Abstract] [Full Text] [PDF]
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S. Bose, J. A. Dutko, and R. S. Zitomer Genetic Factors That Regulate the Attenuation of the General Stress Response of Yeast Genetics, March 1, 2005; 169(3): 1215 - 1226. [Abstract] [Full Text] [PDF]
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S. B. Ferguson, E. S. Anderson, R. B. Harshaw, T. Thate, N. L. Craig, and H. C. M. Nelson Protein Kinase A Regulates Constitutive Expression of Small Heat-Shock Genes in an Msn2/4p-Independent and Hsf1p-Dependent Manner in Saccharomyces cerevisiae Genetics, March 1, 2005; 169(3): 1203 - 1214. [Abstract] [Full Text] [PDF]
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Y. Garten, S. Kaplan, and Y. Pilpel Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data Nucleic Acids Res., January 31, 2005; 33(2): 605 - 615. [Abstract] [Full Text] [PDF]
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J. Zaim, E. Speina, and A. M. Kierzek Identification of New Genes Regulated by the Crt1 Transcription Factor, an Effector of the DNA Damage Checkpoint Pathway in Saccharomyces cerevisiae J. Biol. Chem., January 7, 2005; 280(1): 28 - 37. [Abstract] [Full Text] [PDF]
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E. Durchschlag, W. Reiter, G. Ammerer, and C. Schuller Nuclear Localization Destabilizes the Stress-regulated Transcription Factor Msn2 J. Biol. Chem., December 31, 2004; 279(53): 55425 - 55432. [Abstract] [Full Text] [PDF]
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M. Krantz, B. Nordlander, H. Valadi, M. Johansson, L. Gustafsson, and S. Hohmann Anaerobicity Prepares Saccharomyces cerevisiae Cells for Faster Adaptation to Osmotic Shock Eukaryot. Cell, December 1, 2004; 3(6): 1381 - 1390. [Abstract] [Full Text] [PDF]
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J. W. Loar, R. M. Seiser, A. E. Sundberg, H. J. Sagerson, N. Ilias, P. Zobel-Thropp, E. A. Craig, and D. E. Lycan Genetic and Biochemical Interactions Among Yar1, Ltv1 and RpS3 Define Novel Links Between Environmental Stress and Ribosome Biogenesis in Saccharomyces cerevisiae Genetics, December 1, 2004; 168(4): 1877 - 1889. [Abstract] [Full Text] [PDF]
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B. Schade, G. Jansen, M. Whiteway, K. D. Entian, and D. Y. Thomas Cold Adaptation in Budding Yeast Mol. Biol. Cell, December 1, 2004; 15(12): 5492 - 5502. [Abstract] [Full Text] [PDF]
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S. J. Zanton and B. F. Pugh Changes in genomewide occupancy of core transcriptional regulators during heat stress PNAS, November 30, 2004; 101(48): 16843 - 16848. [Abstract] [Full Text] [PDF]
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L. Viladevall, R. Serrano, A. Ruiz, G. Domenech, J. Giraldo, A. Barcelo, and J. Arino Characterization of the Calcium-mediated Response to Alkaline Stress in Saccharomyces cerevisiae J. Biol. Chem., October 15, 2004; 279(42): 43614 - 43624. [Abstract] [Full Text] [PDF]
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R. M. Marion, A. Regev, E. Segal, Y. Barash, D. Koller, N. Friedman, and E. K. O'Shea Inaugural Article: Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression PNAS, October 5, 2004; 101(40): 14315 - 14322. [Abstract] [Full Text] [PDF]
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L. Wang, G. Renault, H. Garreau, and M. Jacquet Stress induces depletion of Cdc25p and decreases the cAMP producing capability in Saccharomyces cerevisiae Microbiology, October 1, 2004; 150(10): 3383 - 3391. [Abstract] [Full Text] [PDF]
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S. Nicholls, M. Straffon, B. Enjalbert, A. Nantel, S. Macaskill, M. Whiteway, and A. J. P. Brown Msn2- and Msn4-Like Transcription Factors Play No Obvious Roles in the Stress Responses of the Fungal Pathogen Candida albicans Eukaryot. Cell, October 1, 2004; 3(5): 1111 - 1123. [Abstract] [Full Text] [PDF]
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K. A. Kafadar and M. S. Cyert Integration of Stress Responses: Modulation of Calcineurin Signaling in Saccharomyces cerevisiae by Protein Kinase A Eukaryot. Cell, October 1, 2004; 3(5): 1147 - 1153. [Abstract] [Full Text] [PDF]
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D. A. Smith, S. Nicholls, B. A. Morgan, A. J.P. Brown, and J. Quinn A Conserved Stress-activated Protein Kinase Regulates a Core Stress Response in the Human Pathogen Candida albicans Mol. Biol. Cell, September 1, 2004; 15(9): 4179 - 4190. [Abstract] [Full Text] [PDF]
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T. B. Salmon, B. A. Evert, B. Song, and P. W. Doetsch Biological consequences of oxidative stress-induced DNA damage in Saccharomyces cerevisiae Nucleic Acids Res., July 14, 2004; 32(12): 3712 - 3723. [Abstract] [Full Text] [PDF]
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